ArticleChemical physics letters2017
Improved Treatment of Nucleosides and Nucleotides in the OPLS-AA Force Field.
Article in Chemical physics letters, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
8 citing papers in PubMed.
- Mannose Targeting and Hydrophobic Tuning of Polycationic Vectors for Efficient Immunostimulatory CpG Delivery.ACS applied nano materials · 2025Article
- Computational Methods for Modeling Lipid-Mediated Active Pharmaceutical Ingredient Delivery.Molecular pharmaceutics · 2025Review
- Molecular dynamics analysis of biomolecular systems including nucleic acids.Biophysics and physicobiology · 2022Article
- A general RNA force field: comprehensive analysis of energy minima of molecular fragments of RNA.Journal of molecular modeling · 2021Article
- Deconvolution of conformational exchange from Raman spectra of aqueous RNA nucleosides.Communications chemistry · 2020Article
- Article
- Development and Testing of the OPLS-AA/M Force Field for RNA.Journal of chemical theory and computation · 2019Article
- Enhanced Monte Carlo Methods for Modeling Proteins Including Computation of Absolute Free Energies of Binding.Journal of chemical theory and computation · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
DFT calculations have been used to develop improved descriptions of the torsional energetics for nucleosides and nucleotides in the OPLS-AA force field. Scans of nucleotide dihedral angles (γ, χ, and β) and methyl phosphates provided the bases for the new torsional parameters. In addition, the angle-bending parameters of phosphodiesters and ribose were updated, and adjustments were made to existing carbohydrate torsions to better capture the sugar puckering landscape of ribose. MD simulations of nucleosides with the new parameters demonstrate a significant improvement in the ribose sugar puckering and χ angle distributions. Additionally, energy-minimization of protein-nucleotide crystal structures with the new parameters produced accurate poses.
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Registered trials
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